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Is this about having two edmx files with exactly the same sets of entities (including names, namespaces and properties)? Or is it in general a duplicate of
http://entityframework.codeplex.com/workitem/589 where namespaces for POCO types are ignored and therefore you get an exception when having two entities with the same names but different
namespaces since they both match an entity from the model?

This is a duplicate of work item 483 (http://entityframework.codeplex.com/workitem/483). Runtime currently does not support POCO types with the same names for non-Code First
approach. The designer does not show any errors but when you run your app you will get:
Unhandled Exception: System.Data.MetadataException: Schema specified is not valid. Errors:
The mapping of CLR type to EDM type is ambiguous because multiple CLR types match the EDM type 'Country'. Previously found CLR type 'ConsoleApplication19.NewFolder1.Country', newly found CLR type 'ConsoleApplication19.NewFolder2.Country'.